The aim of this study was to assess mycotoxin contamination of crops grown by rural subsistence farmers over two seasons (2011 and 2012) in two districts, Vhembe District Municipality (VDM, Limpopo Province) and Gert Sibande District Municiality (GSDM, Mpumalanga Province), in northern South Africa and to evaluate its impact on farmers' productivity and human and animal health. A total of 114 maize samples were collected from 39 households over the two seasons and were analysed using a validated liquid chromatography-tandem mass spectrometry mycotoxins method. Aflatoxin B1 (AFB1) occurrence ranged from 1 to 133 µg kg(-1) in VDM while AFB1 levels in GSDM were less than 1.0 µg kg(-1) in all maize samples. Fumonisin B1 levels ranged from 12 to 8514 µg kg(-1) (VDM) and 11-18924 µg kg(-1) (GSDM) in 92% and 47% positive samples, respectively, over both seasons. Natural occurrence and contamination with both fumonisins and aflatoxins in stored home-grown maize from VDM was significantly (p < 0.0001) higher than from GSDM over both seasons.

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